Re: [AMBER] Problems with in CpHMD as adding a new titratable ligand

From: Jason Swails <>
Date: Fri, 6 May 2016 18:27:41 -0400

On Fri, May 6, 2016 at 4:43 PM, Yong Wang <> wrote:

> Hi,
> I want to titrate a ligand in complex with a protein. By following the
> section of "Extending constant pH to additional titratable groups" in
> Amber15 manual, I tried to prepare the parameters for Amber14. Now I
> already got the reference pKa, partial charges and reference energy (using
> TI). Then I added the parameters to the file of
> $AMBERHOME/AmberTools/src/etc/cpinutils/

​You need to edit
instead (for AmberTools 16 -- for AmberTools 15, the correct file is

But I suggest upgrading to AmberTools 16, especially if you are having
trouble (as that is the version that gets the best support).

> But I encountered a problem with (python
> ~/software/amber14/bin/
> --describe) to prepare the cpin file. The errors are pasted as below:
> Traceback (most recent call last):
> File "amber14/bin/", line 11, in <module>
> from chemistry.amber import titratable_residues as residues
> File
> "amber14/lib/python2.7/site-packages/chemistry/amber/",
> line 853
> XXX = TitratableResidue('XXX', ['C13','H1', 'C17','H2', 'H3',
> 'C02','N01','H4',
> ^

> SyntaxError: invalid syntax

​This is a Python code, and as such, modifying it requires some experience
coding and debugging Python. A SyntaxError in Python typically means
you've made a typo -- a missing parentheses, quotation mark, comma, etc.
Look for some kind of trivial typo near the marker.


Jason M. Swails
AMBER mailing list
Received on Fri May 06 2016 - 15:30:03 PDT
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